Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	F	L	A	H	L	H	L	A	H	L	A	E	S	S	L	S	G	N	L	L	A	D	F	V	R	G	N	P	E	E	S	F	P	P	D	V	V	A	G	I	H	M	H	R	R	I	D	V	L	T	D	N	L	P	E	V	R	E
Secondary structure
SS confidence
Disorder		?	?																												?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	R	E	W	F	R	S	E	T	R	R	V	A	P	I	T	L	D	V	M	W	D	H	F	L	S	R	H	W	S	Q	L	S	P	D	F	P	L	Q	E	F	V	C	Y	A	R	E	Q	V	M	T	I	L	P	D	S	P	P	R	F
Secondary structure
SS confidence
Disorder																																																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	N	L	N	N	Y	L	W	S	E	Q	W	L	V	R	Y	R	D	M	D	F	I	Q	N	V	L	N	G	M	A	S	R	R	P	R	L	D	A	L	R	D	S	W	Y	D	L	D	A	H	Y	D	A	L	E	T	R	F	W	Q	F
Secondary structure
SS confidence
Disorder																																	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.
Sequence		Y	P	R	M	M	A	Q	A	S	R	K	A	L
Secondary structure
SS confidence
Disorder												?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 1riq chain A domain 1 Region: 102 - 190 Aligned: 78 Modelled: 89 Confidence: 27.5% Identity: 13% Fold: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Superfamily: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Family: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Phyre2 PDB 1s5q chain B Region: 102 - 183 Aligned: 76 Modelled: 82 Confidence: 23.8% Identity: 13% Fold: PAH2 domain Superfamily: PAH2 domain Family: PAH2 domain Phyre2 PDB 1x1n chain A domain 1 Region: 99 - 193 Aligned: 95 Modelled: 95 Confidence: 16.1% Identity: 15% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Amylase, catalytic domain Phyre2 PDB 1r7m chain A domain 1 Region: 15 - 24 Aligned: 10 Modelled: 10 Confidence: 13.5% Identity: 30% Fold: Homing endonuclease-like Superfamily: Homing endonucleases Family: Group I mobile intron endonuclease Phyre2 PDB 1ich chain A Region: 74 - 152 Aligned: 76 Modelled: 79 Confidence: 12.6% Identity: 12% Fold: DEATH domain Superfamily: DEATH domain Family: DEATH domain, DD Phyre2 PDB 1ich chain A Region: 74 - 152 Aligned: 76 Modelled: 79 Confidence: 12.6% Identity: 12% PDB header:apoptosis Chain: A: PDB Molecule:tumor necrosis factor receptor-1; PDBTitle: solution structure of the tumor necrosis factor receptor-12 death domain Phyre2 PDB 1puz chain A Region: 77 - 129 Aligned: 52 Modelled: 53 Confidence: 10.7% Identity: 17% Fold: YgfY-like Superfamily: YgfY-like Family: YgfY-like Phyre2 PDB 1yfs chain B Region: 140 - 190 Aligned: 51 Modelled: 51 Confidence: 10.6% Identity: 14% PDB header:ligase Chain: B: PDB Molecule:alanyl-trna synthetase; PDBTitle: the crystal structure of alanyl-trna synthetase in complex2 with l-alanine Phyre2 PDB 1vhb chain A Region: 85 - 185 Aligned: 92 Modelled: 101 Confidence: 8.9% Identity: 10% Fold: Globin-like Superfamily: Globin-like Family: Globins Phyre2 PDB 2jr5 chain A Region: 77 - 131 Aligned: 54 Modelled: 55 Confidence: 8.9% Identity: 17% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0350 protein vc_2471; PDBTitle: solution structure of upf0350 protein vc_2471. northeast2 structural genomics target vcr36 Phyre2 PDB 3hxx chain A Region: 140 - 186 Aligned: 47 Modelled: 47 Confidence: 8.2% Identity: 11% PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp Phyre2 PDB 1x6i chain B Region: 77 - 131 Aligned: 54 Modelled: 55 Confidence: 7.9% Identity: 17% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ygfy; PDBTitle: crystal structure of ygfy from escherichia coli Phyre2 PDB 1yh2 chain A domain 1 Region: 129 - 191 Aligned: 59 Modelled: 63 Confidence: 7.7% Identity: 15% Fold: UBC-like Superfamily: UBC-like Family: UBC-related Phyre2 PDB 1muk chain A Region: 52 - 93 Aligned: 40 Modelled: 42 Confidence: 7.4% Identity: 28% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 2f05 chain A domain 1 Region: 156 - 183 Aligned: 28 Modelled: 28 Confidence: 7.2% Identity: 21% Fold: PAH2 domain Superfamily: PAH2 domain Family: PAH2 domain Phyre2 PDB 1r7m chain A Region: 9 - 24 Aligned: 16 Modelled: 16 Confidence: 6.6% Identity: 25% PDB header:hydrolase/dna Chain: A: PDB Molecule:intron-encoded endonuclease i-scei; PDBTitle: the homing endonuclease i-scei bound to its dna recognition2 region Phyre2 PDB 2a0b chain A Region: 103 - 192 Aligned: 86 Modelled: 90 Confidence: 6.5% Identity: 8% Fold: Four-helical up-and-down bundle Superfamily: Histidine-containing phosphotransfer domain, HPT domain Family: Aerobic respiration control sensor protein, ArcB Phyre2 PDB 1fad chain A Region: 76 - 152 Aligned: 72 Modelled: 77 Confidence: 6.4% Identity: 11% Fold: DEATH domain Superfamily: DEATH domain Family: DEATH domain, DD Phyre2 PDB 2jyn chain A Region: 166 - 184 Aligned: 19 Modelled: 19 Confidence: 6.0% Identity: 21% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0368 protein ypl225w; PDBTitle: a novel solution nmr structure of protein yst0336 from2 saccharomyces cerevisiae. northeast structural genomics3 consortium target yt51/ontario centre for structural4 proteomics target yst0336 Phyre2 PDB 4a56 chain A Region: 86 - 128 Aligned: 42 Modelled: 43 Confidence: 5.9% Identity: 14% PDB header:protein transport Chain: A: PDB Molecule:pullulanase secretion protein puls; PDBTitle: crystal structure of the type 2 secretion system pilotin2 from klebsiella oxytoca Phyre2 1 d1riqa1 2 d1s5qb_ 3 d1x1na1 4 d1r7ma1 5 d1icha_ 6 c1ichA_ 7 d1puza_ 8 c1yfsB_ 9 d1vhba_ 10 c2jr5A_ 11 c3hxxA_ 12 c1x6iB_ 13 d1yh2a1 14 d1muka_ 15 d2f05a1 16 c1r7mA_ 17 d2a0ba_ 18 d1fada_ 19 c2jynA_ 20 c4a56A_ 21 22 23 24 25

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 d1riqa1 27.5 13 Fold:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Superfamily:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Family:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) 2 d1s5qb_ 23.8 13 Fold:PAH2 domain Superfamily:PAH2 domain Family:PAH2 domain 3 d1x1na1 16.1 15 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 4 d1r7ma1 13.5 30 Fold:Homing endonuclease-like Superfamily:Homing endonucleases Family:Group I mobile intron endonuclease 5 d1icha_ 12.6 12 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD 6 c1ichA_ 12.6 12 PDB header:apoptosis Chain: A: PDB Molecule:tumor necrosis factor receptor-1; PDBTitle: solution structure of the tumor necrosis factor receptor-12 death domain 7 d1puza_ 10.7 17 Fold:YgfY-like Superfamily:YgfY-like Family:YgfY-like 8 c1yfsB_ 10.6 14 PDB header:ligase Chain: B: PDB Molecule:alanyl-trna synthetase; PDBTitle: the crystal structure of alanyl-trna synthetase in complex2 with l-alanine 9 d1vhba_ 8.9 10 Fold:Globin-like Superfamily:Globin-like Family:Globins 10 c2jr5A_ 8.9 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0350 protein vc_2471; PDBTitle: solution structure of upf0350 protein vc_2471. northeast2 structural genomics target vcr36 11 c3hxxA_ 8.2 11 PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp 12 c1x6iB_ 7.9 17 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ygfy; PDBTitle: crystal structure of ygfy from escherichia coli 13 d1yh2a1 7.7 15 Fold:UBC-like Superfamily:UBC-like Family:UBC-related 14 d1muka_ 7.4 28 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 15 d2f05a1 7.2 21 Fold:PAH2 domain Superfamily:PAH2 domain Family:PAH2 domain 16 c1r7mA_ 6.6 25 PDB header:hydrolase/dna Chain: A: PDB Molecule:intron-encoded endonuclease i-scei; PDBTitle: the homing endonuclease i-scei bound to its dna recognition2 region 17 d2a0ba_ 6.5 8 Fold:Four-helical up-and-down bundle Superfamily:Histidine-containing phosphotransfer domain, HPT domain Family:Aerobic respiration control sensor protein, ArcB 18 d1fada_ 6.4 11 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD 19 c2jynA_ 6.0 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0368 protein ypl225w; PDBTitle: a novel solution nmr structure of protein yst0336 from2 saccharomyces cerevisiae. northeast structural genomics3 consortium target yt51/ontario centre for structural4 proteomics target yst0336 20 c4a56A_ 5.9 14 PDB header:protein transport Chain: A: PDB Molecule:pullulanase secretion protein puls; PDBTitle: crystal structure of the type 2 secretion system pilotin2 from klebsiella oxytoca 21 d1rg6a_ not modelled 5.6 24 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain 22 c2yqfA_ not modelled 5.3 13 PDB header:protein binding Chain: A: PDB Molecule:ankyrin-1; PDBTitle: solution structure of the death domain of ankyrin-1 23 c1ztaA_ not modelled 5.2 26 PDB header:dna-binding motif Chain: A: PDB Molecule:leucine zipper monomer; PDBTitle: the solution structure of a leucine-zipper motif peptide 24 d2incc1 not modelled 5.2 40 Fold:beta-Grasp (ubiquitin-like) Superfamily:TmoB-like Family:TmoB-like 25 d1svda2 not modelled 5.1 42 Fold:Ferredoxin-like Superfamily:RuBisCO, large subunit, small (N-terminal) domain Family:Ribulose 1,5-bisphosphate carboxylase-oxygenase

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0